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Dose absorption of Omicron variant SARS-CoV-2 by electron radiation: Using Geant4-DNA toolkit

  • Mehrdad Jalili Torkamani (Department of Physics, Faculty of Science, University of Mohaghegh Ardabili) ;
  • Chiman Karami (Department of Microbiology, Parasitology and Immunology, Ardabil University of Medical Sciences) ;
  • Pooneh Sayyah-Koohi (Department of Physics, Faculty of Science, University of Mohaghegh Ardabili) ;
  • Farhood Ziaie (Radiation Application Research School, Nuclear Science & Technology Research Institute) ;
  • Seyyedsina Moosavi (Department of Geology, Ferdowsi University of Mashhad) ;
  • Farhad Zolfagharpour (Department of Physics, Faculty of Science, University of Mohaghegh Ardabili)
  • Received : 2023.03.16
  • Accepted : 2024.01.31
  • Published : 2024.06.25

Abstract

In this research, the Omicron variant of the SARS-CoV-2 virus was simulated and exposed to electron radiation with up to 20 keV energy. Absorbed energy was measured for spike protein, nucleocapsid protein, and envelope of the virus. Simulations were performed by Geant4-DNA in a water environment at temperature of 20 ℃ and pressure of 1 atm. Since the viral RNA is kept inside the nucleocapsid protein, damage to this area could destroy the viral RNA strand and create an inactive virus. Our findings showed that electron beams with an energy of 2.5 keV could cause a maximum absorption dose and consequently maximum damage to the nucleocapsid and effectively be used for inactivation virus.

Keywords

Acknowledgement

The authors would like to acknowledge staff of nuclear lab of University of Mohaghegh Ardabili to giving allow access to their computer and their intellectual cooperation in this study.

References

  1. H. Aboubakr, et al., Stability of SARS-CoV-2 and other coronaviruses in the environment and on common touch surfaces and the influence of climatic conditions: a review, Transboundary and Emerging Diseases 68 (2) (2021) 296-312. https://doi.org/10.1111/tbed.13707
  2. S. Alsobaie, Understanding the molecular biology of SARS-CoV-2 and the COVID19 pandemic: a review, Infect. Drug Resist. 14 (2019) 2259-2268. https://doi.org/10.2147/IDR.S306441
  3. Q. Yang, et al., Structural analysis of the SARS-CoV-2 omicron variant proteins, Research (2021) 9769586.
  4. I. Seah, X. Su, G. Lingam, Revisiting the dangers of the coronavirus in the ophthalmology practice, Eye (Lond) 34 (7) (2020) 1155-1157. https://doi.org/10.1038/s41433-020-0790-7
  5. Y. Yuan, et al., Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains, Nat. Commun. 8 (2017) 15092.
  6. J. Lan, et al., Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor, Nature 581 (7807) (2020) 215-220. https://doi.org/10.1038/s41586-020-2180-5
  7. Z. Liu, et al., Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS-CoV-2, J. Med. Virol. 92 (6) (2020) 595-601. https://doi.org/10.1002/jmv.25726
  8. A. Mittal, et al., COVID-19 pandemic: insights into structure, function, and hACE2 receptor recognition by SARS-CoV-2, PLoS Pathog. 16 (8) (2020) e1008762.
  9. R. Yan, et al., Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2, Science 367 (6485) (2020) 1444-1448. https://doi.org/10.1126/science.abb2762
  10. T. Biftu, R. SinhaRoy, DPP-4 inhibitors, in: Comprehensive Medicinal Chemistry III, 2017, pp. 512-555.
  11. J. Yang, et al., Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor, Nat. Commun. 11 (1) (2020) 4541.
  12. S. Pascarella, et al., The electrostatic potential of the Omicron variant spike is higher than in Delta and Delta-plus variants: a hint to higher transmissibility? J. Med. Virol. 94 (4) (2022) 1277-1280. https://doi.org/10.1002/jmv.27528
  13. E.I. Patterson, et al., Methods of inactivation of SARS-CoV-2 for downstream biological assays, J. Infect. Dis. 222 (9) (2020) 1462-1467. https://doi.org/10.1093/infdis/jiaa507
  14. G. Xiling, et al., In vitro inactivation of SARS-CoV-2 by commonly used disinfection products and methods, Sci. Rep. 11 (1) (2021) 2418.
  15. P.F.S. Pereira, et al., Inactivation of SARS-CoV-2 by a chitosan/alpha-Ag2WO4 composite generated by femtosecond laser irradiation, Sci. Rep. 12 (1) (2022) 8118.
  16. A. Fadaei, N. Nakhostin Ansari, Viral inactivation with emphasis on SARS-CoV-2 using physical and chemical disinfectants, Sci. World J. 2021 (2021) 1-6. https://doi.org/10.1155/2021/9342748
  17. M. Durante, et al., Virus irradiation and COVID-19 disease, Frontier. Phys. 8 (2020).
  18. A. Leung, et al., In vitro inactivation of SARS-CoV-2 using gamma radiation, Appl Biosaf 25 (3) (2020) 157-160. https://doi.org/10.1177/1535676020934242
  19. F. Liu, et al., SARS-CoV-2 inactivation simulation using 14 MeV neutron irradiation, Life 11 (12) (2021).
  20. Z. Francis, et al., Monte Carlo simulation of SARS-CoV-2 radiation-induced inactivation for vaccine development, Radiat. Res. 195 (3) (2021) 221-229. https://doi.org/10.1667/RADE-20-00241.1
  21. R.W.N. Mark Plavsic, Efficacy of electron beam for viral inactivation, J. Microb. Biochem. Technol. 7 (4) (2015).
  22. S. Shahi, et al., Review of proposed different irradiation methods to inactivate food-processing viruses and microorganisms, Food Sci. Nutr. 9 (10) (2021) 5883-5896. https://doi.org/10.1002/fsn3.2539
  23. M.A. Bernal, et al., Track structure modeling in liquid water: a review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit, Phys. Med. 31 (8) (2015) 861-874. https://doi.org/10.1016/j.ejmp.2015.10.087
  24. S. Incerti, et al., Comparison of GEANT4 very low energy cross section models with experimental data in water, Med. Phys. 37 (9) (2010) 4692-4708. https://doi.org/10.1118/1.3476457
  25. S. Agostinelli, et al., Geant4-a simulation toolkit, Nucl. Instrum. Methods Phys. Res. Sect. A Accel. Spectrom. Detect. Assoc. Equip. 506 (3) (2003) 250-303. https://doi.org/10.1016/S0168-9002(03)01368-8
  26. S. Incerti, et al., Energy deposition in small-scale targets of liquid water using the very low energy electromagnetic physics processes of the Geant4 toolkit, Nucl. Instrum. Methods Phys. Res. Sect. B Beam Interact. Mater. Atoms 306 (2013) 158-164. https://doi.org/10.1016/j.nimb.2012.12.054
  27. S. Incerti, et al., The geant4-DNA project, Int. J. Model. Simul. Sci. Comput. 1 (2010).
  28. S. Incerti, et al., Review of Geant4-DNA applications for micro and nanoscale simulations, Phys. Med. 32 (10) (2016) 1187-1200. https://doi.org/10.1016/j.ejmp.2016.09.007
  29. S. Incerti, et al., The geant4-DNA project, Int. J. Model., Simulat., Sci. Comput. 1 (2) (2012) 157-178. https://doi.org/10.1142/S1793962310000122
  30. P. Rafiepour, S. Sina, S.M.J. Mortazavi, Inactivation of SARS-CoV-2 by charged particles for future vaccine production applications: a Monte Carlo study, Radiat. Phys. Chem. Oxf. Engl. 198 (2022) 110265, 1993.
  31. Severine Duvaud, Chiara Gabella, Frederique Lisacek, Heinz Stockinger, Vassilios Ioannidis, Christine Durinx, Expasy, the Swiss Bioinformatics resource portal, as designed by its users, Nucleic Acids Res. 49 (W1) (2 July 2021) W216-W227. https://doi.org/10.1093/nar/gkab225
  32. L. Zhao, et al., A generalized target theory and its applications, Sci. Rep. 5 (2015) 14568.
  33. H. Wulf, et al., Heavy-Ion effects on mammalian cells: inactivation measurements with different cell lines, Radiation Res. 104 (1985) 122-134.
  34. The international commission on radiation units and measurements, J. ICRU 11 (1) (2011). Report 85.
  35. A. Bardane, et al., Monte Carlo simulation method highlighting on the electron beam irradiation on the structure of SARS-CoV-2, Moscow Univ. Phys. Bull. 75 (6) (2021) 638-644. https://doi.org/10.3103/S0027134920060041
  36. G. Feng, et al., Electron beam irradiation on novel coronavirus (COVID-19): a Monte-Carlo simulat ion, Chin. Phys. B 29 (4) (2020) 048703.